Denis Schapiro's repositories
awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
basic-illumination
ImageJ BaSiC shading correction for use with Ashlar
CyCif_Manager
Manage CyCIF Pipeline on HMS O2
histoCAT
Histology Topography Cytometry Analysis Toolbox
cytokit
Microscopy Image Cytometry Toolkit
IMCWorkflow
Overview repository on IMC data analysis
mcmicro
Multiple Choice Microscopy
mcmicro-1
Multiple-choice microscopy pipeline
miti-consortium.org
MITI Consortium website
napari
napari: a fast, interactive, multi-dimensional image viewer for python
neighbouRhood
Adds an R implementation for the HistoCAT neightbourhood analysis that runs from CellProfiler output.
nextflow
A DSL for data-driven computational pipelines
pca_analysis_toolkit
Analysis toolkit for exploratory analyses in the Pre-Cancer Atlas project
ripgrep
ripgrep recursively searches directories for a regex pattern while respecting your gitignore
scanpy
Single-Cell Analysis in Python. Scales to >1M cells.